1. Nguyen B, Gurusinga F, Mettal U, Schäberle T, Yokoyama K. Radical-Mediated Nucleophilic Peptide Cross-Linking in Dynobactin Biosynthesis. J. Am. Chem. Soc. 2024, 146, 46, 31715–31732, doi.org/10.1021/jacs.4c10425.
2. Du Y, Thanapipatsiri A, Yokoyama K. Biosynthesis and Genome Mining Potentials of Nucleoside Natural Products. ChemBioChem 2023, 24, e202300342.
3. Böhringer N, Kramer JC, de la Mora E, Padva L, Wuisan ZG, Liu Y, Kurz M, Marner M, Nguyen H, Amara P, Yokoyama K, Nicolet Y, Mettal U, Schäberle TF., Genome- and metabolome-guided discovery of marine BamA inhibitors revealed a dedicated darobactin halogenase. Cell Chem Biol. 2023, S2451-9456(23) 00193-9.
4. Nguyen, H.; Kresna, I. D. M.; Böhringer, N.; Ruel, J.; Mora, E. de la; Kramer, J.- C.; Lewis, K.; Nicolet, Y.; Schäberle, T. F.;
   Yokoyama, K.*, Characterization of a Radical SAM Oxygenase for the Ether Crosslinking in Darobactin Biosynthesis, J. Am. Chem. Soc. 2022, 144, 41, 18876–18886, doi.org/10.1021/jacs.2c05565
5. Ren, Z.#; Chhetri, A.#; Guan, Z.; Suo, Y.; Yokoyama, K.*; Lee, S.-Y.* Structural basis for inhibition and regulation of a chitin synthase from Candida albicans. Nat Struct Mol Biol. 2022 Jul;29(7):653-664. doi: 10.1038/s41594-022-00791-x. (# co-first authorship. * co-correspondence)
6. Draelos, M. M.; Thanapipatsiri, A.; Du, Y.;Yokoyama, K.; Cryptic Phosphorylation-Mediated Divergent Biosynthesis of High-Carbon Sugar Nucleoside Antifungals. ACS Chem Biol 2022, 17, 898-907. doi: 10.1021/acschembio.1c00971.
7. Cáceres, J. C.; Bailey, C.A.; Yokoyama, K.; Greene B. L.; Selenocysteine substitutions in thiyl radical enzymes. Methods Enzymol 2022, 662, 119-141. doi: 10.1016/bs.mie.2021.10.014.
8. Yokoyama, K.; Li, D.#; and Pang, H.#; Resolving the Multidecade-Long Mystery in MoaA Radical SAM Enzyme Reveals New Opportunities to Tackle Human Health Problems. ACS Bio Med Chem Au, 2022 Apr 20;2(2):94-108. (# equal contribution)
9. Pang, H.; Walker, L. M.; Silakov, A.; Zhang, P.; Yang, W.; Elliott, S. J.; Yokoyama, K.; Mechanism of Reduction of an Aminyl Radical Intermediate in the Radical SAM GTP 3′,8-Cyclase MoaA. J. Am. Chem. Soc. 2021, 143, 34, 13835–13844. Highlighted in the JACS Spotlight.
10. Draelos, M. M.#; Thanapipatsiri, A.#; Yokoyama, K; Conserved mechanism of 2′-phosphorylation-aided amide ligation in peptidyl nucleoside biosynthesis. Biochemistry 2021, 60, 2231–2235. DOI:10.1021/acs.biochem.1c00327. (# equal contribution)
11. Chhetri, A., Loksztejn, A. and Yokoyama, K. Quantitative Characterization of the Amount and Length of (1,3)-β-D-glucan for Functional and Mechanistic Analysis of Fungal (1,3)-β-D-glucan Synthase. Bio-protocol 2021, 11(8): e3995. DOI: 10.21769/BioProtoc.3995.
12. Draelos, M. M.; Thanapipatsiri, A.; Sucipto, H.; Yokoyama, K; Cryptic phosphorylation in nucleoside natural product biosynthesis. Nature Chemical Biology 2021, 17, 213-221, DOI: 10.1038/s41589-020-00656-8.  
13. Yokoyama, K., Radical-Mediated Carbon Skeleton Formation in Cofactor and Natural Product Biosynthesis. Comprehensive Natural Products III (Third Ed.) 2020, 5, 70-95, DOI: 10.1016/B978-0-12-409547-2.14745-6. 
14. Draelos M.; Yokoyama K., Biosynthesis and mechanism of action of antifungal peptidyl nucleoside natural products. Comprehensive Natural Products III (Third Ed.) 2020, 2, 613-641, DOI: 10.1016/B978-0-12-409547-2.14680-3.
15. Pang H, Lilla EA, Zhang P, Zhang D, Shields TP, Scott LG, Yang W, Yokoyama K. (2020) Mechanism of rate acceleration of radical C-C bond formation reaction by a radical SAM GTP 3′,8-cyclase. J. Am. Chem. Soc. 2020, 142, 20, 9314–9326.
16. Chhetri A, Loksztejn A, Nguyen H, Pianalto KM, Kim MJ, Hong J, Alspaugh JA, Yokoyama K. (2020) Length specificity and polymerization mechanism of (1,3)-β-D-glucan synthase in fungal cell wall biosynthesis. Biochemistry 2020, 59, 5, 682-693.

17. Yang H, McDaniel E, Impano S, Byer AS, Jodts RJ, Yokoyama K, Broderick WE, Broderick JB, Hoffman BM. (2019) The Elusive 5′-Deoxyadenosyl Radical: Captured and Characterized by EPR and ENDOR Spectroscopies. J Am Chem Soc 2019, 141(30):12139-12146. doi: 10.1021/jacs.9b05926.

18. Nguyen HP, and Yokoyama K (2019). Characterization of Acyl Carrier Protein-Dependent Glycosyltransferase in Mitomycin C Biosynthesis. Biochemistry 2019, 58, 25, 2804–2808.
    
19. Kuhnert E, Li Y, Lan N, Yue Q, Chen L, Cox RJ, An Z, Yokoyama K, Bills GF. Enfumafungin synthase represents a novel lineage of fungal triterpene cyclases. Environ Microbiol 2018, 20, 3325-3342. doi: 10.1111/1462-2920.14333.
20. Byer, A.; Yang, H.; McDaniel, E.; Kathiresan, V.; Impano, S.; Pagnier, A.; Watts, H.; Denler, C.; Vagstad, A.; Piel, J.; Duschene, K.; Shepard, E.; Shields, T.; Scott, L.; Lilla, E.; Yokoyama, K.; Broderick, W.; Hoffman, B.; Broderick, J. (2018), A paradigm shift for radical SAM reactions: The organometallic intermediate Ω is central to catalysis. J. Am. Chem. Soc, 140, 8634-8638.
21. Pang H, and Yokoyama K. (2018) Lessons From the Studies of a C-C Bond Forming Radical SAM Enzyme in Molybdenum Cofactor Biosynthesis. Methods in Enzymology 606, 485-522. doi:10.1016/bs.mie.2018.04.014.
22. Yokoyama K, and Lilla EA. (2018). C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products. Natural Product Reports 18, 35, 660-694. doi: 10.1039/c8np00006a. 
23. Yokoyama K. (2018). Radical Breakthroughs in Natural Product and Cofactor Biosynthesis. Biochemistry 57, 390–402. doi:10.1021/acs.biochem.7b00878.
24. Lilla EA, Yokoyama K. (2016). Carbon extension in peptidylnucleoside biosynthesis by radical SAM enzymes. Nature Chemical Biology 12, 905-907. doi:10.1038/nchembio.2187.
25. Chen L, Li Y, Yue Q, Loksztejn A, Yokoyama K, Felix EA, Liu X, Zhang N, An Z, Bills GF. (2016), Engineering of new pneumocandin side-chain analogues from Glarea lozoyensis by mutasynthesis and evaluation of their antifungal activity, ACS Chem Biol 11, 2724-2733, DOI 10.1021/acschembio.6b00604.
26. Hover BM, Lilla EA, Yokoyama K. (2015). Mechanistic Investigation of cPMP Synthase in Molybdenum Cofactor Biosynthesis Using an Uncleavable Substrate Analogue. Biochemistry, 54, 7229-36.
27. Hover BM, Tonthat NK, Schumacher MA, Yokoyama K. (2015).  Mechanism of pyranopterin ring formation in molybdenum cofactor biosynthesis.  Proc. Natl. Acad. Sci. U. S. A., 112, 6347-52.
28. Yokoyama K, Leimkühler S. (2015)  The role of FeS clusters for molybdenum cofactor biosynthesis and molybdoenzymes in bacteria.  Biochimica et Biophysica Acta. 1853(6):1335-49.
29. Hover BM, Yokoyama K. (2015). C-Terminal glycine-gated radical initiation by GTP 3′,8-cyclase in the molybdenum cofactor biosynthesis.  J. Am. Chem. Soc. 137(9):3352-9.  (Selected for the JACS young investigators virtual issue)
30. Hover B. M.; Losztejn, A.; Ribeiro, A. A.; Yokoyama, K., (2013). Identification of a cyclic nucleotide as a cryptic intermediate in molybdenum cofactor biosynthesis, J. Am. Chem. Soc., 135, 7019 – 7032. PMCID: PMC3777439.  (Recommended by the F1000Prime)

Prior to Duke

1. Ravichandran, K., Minnihan, E. C., Lin, Q., Yokoyama, K., Taguchi, A. T., Shao, J., Nocera, D. G., Stubbe, J., Glutamate 350 plays an essential role in conformational gating of long-range radical transport in Escherichia coli class Ia ribonucleotide reductase, Biochemistry2017, 56, 856-868.
2. Wei, Y.; Mathies, G.; Yokoyama, K.; Chen, J.; Griffin R. G.; Stubbe, J. (2014) A chemically competent thiosulfuranyl radical on the Escherichia coli class III ribonucleotide reductase. J Am Chem Soc. 136, 9001-13.
3. Wörsdörfer, B.; Conner, D. A.; Yokoyama, K.; Livada, J.; Seyedsayamdost, M.; Jiang, W.; Silakov, A.; Stubbe, J.; Bollinger, J. M. Jr.; Krebs, C., (2013) Function of the Diiron Cluster of Escherichia coli Class Ia Ribonucleotide Reductase in Proton-Coupled Electron Transfer, J. Am. Chem. Soc., DOI: 10.1021/ja401342s. PMID: 23676140
4. Ando, N.; Brignole, E.; Zimanyi, C. M.; Funk, M.; Yokoyama, K.; Asturias, F. J.; Stubbe, J.; Drennan, C., (2011). Structural interconversions modulate activity of E. coli ribonucleotide reductase, Proc. Natl. Acad. Sci. U. S. A., 108, 21046–21051.  PMCID: PMC3248520
5. Yokoyama, K., Smith, A. A., Corzilius, B., Griffin, R. G.; Stubbe, J., (2011). Equilibration of tyrosyl radicals (Y356•, Y731•, Y730•) in the radical propagation pathway of the E. coli class Ia ribonucleotide reductase. J. Am. Chem. Soc., 133, 18420–18432.  PMCID: PMC3236566
6. Yokoyama, K., Uhlin, U., and Stubbe, J., (2010). A hot oxidant, 3-NO2Y122 radical, unmasks conformational gating in ribonucleotide reductase. J. Am. Chem. Soc., 132, 15368–15379. PMCID: PMC3005585
7. Yokoyama, K., Uhlin, U., and Stubbe, J., (2010). Site-specific incorporation of 3-nitrotyrosine as a probe of pKa perturbation of redox active tyrosines in ribonucleotide reductase. J. Am. Chem. Soc., 132, 8385–8397. PMCID:  PMC2905227
8. Minnihan, E. C., Yokoyama, K., Stubbe, J., (2009). Unnatural amino acid: better than the real thing? F1000 Biology Reports, 1:88, doi: 10.3410/B1-88.
9. Artin, E., Wang, J., Lohman, G. J., Yokoyama, K., Yu, G., Griffin, R.G., Bar, G. and Stubbe J., (2009). Insight into the mechanism of inactivation of ribonucleotide reductase by gemcitabine 5’-diphosphate in the presence or absence of reductant. Biochemistry, 48, 11622–11629.  PMCID: PMC2917094
10. Kudo, F., Kawashima, T., Yokoyama, K., Eguchi, T., (2009). Enzymatic Preparation of Neomycin C from Ribostamycin. J. Antibiot., 62, 643–646.
11. Yokoyama, K.; Ohmori, D.; Kudo, F.; Eguchi, T., (2008). Mechanistic Study on the Reaction of a Radical SAM Dehydrogenase BtrN by EPR Spectroscopy. Biochemistry 47, 8950-8960.
12. Yokoyama, K.; Yamamoto, Y.; Kudo, F.; Eguchi, T., (2008). Involvement of Two Distinct N-Acetyl Glucosaminyltransferases and a Dual Functional Deacetylase in the Neomycin Biosynthesis. ChemBioChem, 9, 865-869.
13. Yokoyama, K., Numakura, M.a, Kudo, F., Ohmori, D.; Eguchi, T., (2007). Characterization and Mechanistic Study of a Radical SAM Dehydrogenase in the Biosynthesis of Butirosin.  J. Am. Chem. Soc., 129, 15147-15155.
14. Yokoyama, K., Kudo, F., Kuwahara, M., Inomata, K., Tamegai, H., Eguchi, T., Kakinuma, K., (2005) Stereochemical Recognition of Doubly Functional Aminotransferase in 2-Deoxystreptamine Biosynthesis. J. Am. Chem. Soc., 127, 5869-5874.
15. Kudo, F., Yamamoto, Y., Yokoyama, K., Eguchi, T., Kakinuma, K., (2005). Biosynthesis of 2-Deoxystreptamine by Three Crucial Enzymes in Streptomyces fradiae NBRC 12773. J. Antibiot., 58, 766-774.

Complete List of Published Work in MyBibliography